In a message to poet Ashok Vajpeyi, Raza's close friend, Mukherjee said, "In his death, the nation has lost a highly creative and acclaimed artist.
"His death leaves a void in the world of art and creativity which will be difficult to fill," he said.
Modi said he was saddened by the demise of Raza "whose contribution to art will always be remembered".
Congress President Sonia Gandhi described his death as a huge loss for the world of art and the country.
94-year-old Raza was suffering from age-related ailments and was in the ICU of a private hospital here for the last two months.
An internationally-acclaimed painter, Raza was honoured with the Padma Shri.